Phineas Welles is Frank Nolta. I may be misremembering that name, so I'll just call him Frank.
Here's what's in the game: On board the Hope, nine years into their ten-year long voyage, the crew discovers that their skip drive is inoperable. It will take them another twenty-six years to reach Halcyon at sub-light speeds, and they only have enough food to last them another year. Unbeknownst to the others, Frank, the chief mechanic, starts thawing and eating the bodies of frozen colonists. When the others discover this, half of them side with Frank and the other half side with the captain, Hunte. When last we hear of them via ship's logs, Hunte has gone to confront Frank. We do not find out what happened between them, but we do know that the Hope eventually arrived in Halcyon.
Here's my theory: Frank was the sole survivor of the Hope, and he lived off the corpses of the colonists for twenty-six years. When he arrived in Halcyon, he led the Board to the Hope, but they were unwilling to revive the colonists. Frank, consumed by guilt, made it his mission to revive them by any means necessary. This put him at odds with the Board, who, when they discovered that Frank had been experimenting on the colonists in hopes of finding a way to revive them, declared him a murderer and a traitor.
Frank, as chief engineer of the Hope, would have the technological skill that Phineas Welles displays. He would have a motivation to revive the colonists: atoning for his guilt. In the first log entry on the Hope that is ascribed to Welles, he appears to make up his name on the spot: "P. Welles... yes, that'll do." We don't get any other backstory for Dr. Welles, odd for such a central character. The timeline adds up. Any thoughts?